Starting /dee2/code/volunteer_pipeline.sh ERR6133511 current disk space = 1544390520832 free memory = 1599923100 ERR6133511 SRAfilesize 420e6608ebada7563475618d83293b71 ERR6133511.sra ERR6133511.sra file validated ERR6133511 is single end ERR6133511 is conventional basespace ERR6133511 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133511_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70-93 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.564 37.0 37.0 37.0 37.0 37.0 2 36.8495 37.0 37.0 37.0 37.0 37.0 3 36.53725 37.0 37.0 37.0 37.0 37.0 4 35.89625 37.0 37.0 37.0 33.0 37.0 5 36.014 37.0 37.0 37.0 33.0 37.0 6 36.27825 37.0 37.0 37.0 33.0 37.0 7 38.28525 40.0 37.0 40.0 37.0 40.0 8 38.30225 40.0 37.0 40.0 37.0 40.0 9 38.3545 40.0 37.0 40.0 37.0 40.0 10-11 38.34075 40.0 37.0 40.0 37.0 40.0 12-13 38.2435 40.0 37.0 40.0 37.0 40.0 14-15 38.20375 40.0 37.0 40.0 37.0 40.0 16-17 38.11425 40.0 37.0 40.0 37.0 40.0 18-19 38.069375 40.0 37.0 40.0 37.0 40.0 20-21 38.063875 40.0 37.0 40.0 37.0 40.0 22-23 38.16825 40.0 37.0 40.0 37.0 40.0 24-25 38.040375 40.0 37.0 40.0 37.0 40.0 26-27 38.002624999999995 40.0 37.0 40.0 37.0 40.0 28-29 38.054625 40.0 37.0 40.0 37.0 40.0 30-31 38.0295 40.0 37.0 40.0 37.0 40.0 32-33 38.091499999999996 40.0 37.0 40.0 37.0 40.0 34-35 38.077125 40.0 37.0 40.0 37.0 40.0 36-37 37.955749999999995 37.0 37.0 40.0 37.0 40.0 38-39 37.806 37.0 37.0 40.0 37.0 40.0 40-41 37.6315 37.0 37.0 40.0 37.0 40.0 42-43 37.624875 37.0 37.0 40.0 37.0 40.0 44-45 37.39675 37.0 37.0 40.0 35.0 40.0 46-47 37.255375 37.0 37.0 40.0 33.0 40.0 48-49 37.082875 37.0 37.0 38.5 33.0 40.0 50-51 36.848875 37.0 37.0 37.0 33.0 40.0 52-53 36.44625 37.0 37.0 37.0 33.0 40.0 54-55 36.49925 37.0 37.0 37.0 33.0 40.0 56-57 36.399 37.0 37.0 37.0 33.0 38.5 58-59 36.018375000000006 37.0 37.0 37.0 33.0 37.0 60-61 36.138999999999996 37.0 37.0 37.0 33.0 37.0 62-63 35.989625000000004 37.0 37.0 37.0 33.0 37.0 64-65 35.932625 37.0 37.0 37.0 33.0 37.0 66-67 35.861000000000004 37.0 37.0 37.0 33.0 37.0 68-69 35.001625000000004 35.0 35.0 37.0 33.0 37.0 70-71 35.20005165289256 37.0 33.0 37.0 33.0 37.0 72-73 35.67411462525688 37.0 35.0 37.0 33.0 37.0 74-75 35.647208515560706 37.0 35.0 37.0 33.0 37.0 76-77 35.54212342696292 37.0 33.0 37.0 33.0 37.0 78-79 35.450893346317436 37.0 33.0 37.0 33.0 37.0 80-81 35.44428173348968 37.0 33.0 37.0 33.0 37.0 82-83 35.238635191949626 37.0 33.0 37.0 33.0 37.0 84-85 35.15562988157812 37.0 33.0 37.0 33.0 37.0 86-87 35.129139922978176 37.0 33.0 37.0 33.0 37.0 88-89 35.094351732991015 37.0 33.0 37.0 33.0 37.0 90-91 35.08331193838254 37.0 33.0 37.0 33.0 37.0 92-93 34.95699614890886 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 3.0 21 0.0 22 2.0 23 3.0 24 7.0 25 9.0 26 10.0 27 6.0 28 19.0 29 24.0 30 31.0 31 37.0 32 57.0 33 56.0 34 97.0 35 283.0 36 1077.0 37 1433.0 38 834.0 39 12.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.275 2.9749999999999996 3.2 5.55 2 74.02499999999999 15.25 6.6000000000000005 4.125 3 35.525 39.050000000000004 14.649999999999999 10.775 4 33.175 28.15 18.275 20.4 5 24.9 29.549999999999997 27.525 18.025 6 19.15 38.775 25.05 17.025000000000002 7 36.825 29.2 19.775000000000002 14.2 8 30.049999999999997 32.15 22.8 15.0 9 27.35 29.2 26.85 16.6 10-11 24.725 27.987499999999997 29.2375 18.05 12-13 27.0625 26.775 28.1625 18.0 14-15 21.987499999999997 31.874999999999996 28.3625 17.775 16-17 24.05 31.85 26.025 18.075 18-19 22.6875 27.9125 29.1625 20.2375 20-21 24.478059757469683 26.540817602200274 28.391048881110137 20.5900737592199 22-23 28.000000000000004 23.6875 27.325 20.9875 24-25 24.6 26.0625 28.9875 20.349999999999998 26-27 24.087500000000002 26.1 31.3 18.512500000000003 28-29 25.587500000000002 27.775 27.075 19.5625 30-31 27.3375 27.0875 26.950000000000003 18.625 32-33 24.762500000000003 26.75 28.1375 20.349999999999998 34-35 23.200000000000003 28.425 27.737499999999997 20.6375 36-37 25.2625 24.85 28.287499999999998 21.6 38-39 26.95336917114639 24.8906113264158 30.26628328541068 17.889736217027128 40-41 27.494373593398347 25.243810952738183 26.84421105276319 20.417604401100277 42-43 25.431357839459867 28.294573643410853 27.11927981995499 19.154788697174293 44-45 24.1125 26.375 29.9875 19.525000000000002 46-47 24.325 24.825 29.599999999999998 21.25 48-49 24.125 24.9 31.112499999999997 19.8625 50-51 23.893473368342086 26.84421105276319 29.507376844211052 19.754938734683673 52-53 24.692288369756344 28.422506907812107 27.09118311981914 19.794021602612407 54-55 24.325 28.625 29.2375 17.8125 56-57 25.887500000000003 25.825 28.925 19.3625 58-59 25.3 25.7625 28.025 20.9125 60-61 24.0625 25.724999999999998 31.412499999999998 18.8 62-63 21.6125 28.5875 31.4625 18.337500000000002 64-65 23.175 28.9375 29.9 17.9875 66-67 23.6375 27.5625 29.2375 19.5625 68-69 21.825 27.9125 28.487499999999997 21.775 70-71 23.608157137495308 26.623295383460526 28.625046916051545 21.143500562992617 72-73 25.1696406132194 25.081678813772307 29.50490072882634 20.243779844181955 74-75 24.536394600731676 26.718809133341743 29.847357133846348 18.897439132080233 76-77 22.697910069664346 26.092463584547183 29.119696010132994 22.089930335655477 78-79 23.274111675126903 26.6751269035533 31.040609137055835 19.01015228426396 80-81 22.76774357669804 30.08140422284406 29.35639786313915 17.79445433731875 82-83 24.046434494195687 25.84513330781987 29.79971935195816 20.30871284602628 84-85 22.536835361947468 23.984625240230624 33.235105701473415 20.243433696348497 86-87 22.297817715019256 27.188703465982027 30.654685494223365 19.858793324775352 88-89 21.322207958921695 28.369704749679077 30.449293966623873 19.858793324775352 90-91 25.827984595635428 26.752246469833118 28.960205391527598 18.459563543003853 92-93 22.09242618741977 29.845956354300384 29.62772785622593 18.433889602053917 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.5 16 0.5 17 6.5 18 7.0 19 1.5 20 2.0 21 2.5 22 3.0 23 3.5 24 4.0 25 5.5 26 7.0 27 10.5 28 16.5 29 18.5 30 21.5 31 29.5 32 42.0 33 53.0 34 64.0 35 79.5 36 98.5 37 140.5 38 196.5 39 211.0 40 224.0 41 216.5 42 226.5 43 268.0 44 227.0 45 209.0 46 229.5 47 222.5 48 203.5 49 177.0 50 167.0 51 171.5 52 155.5 53 138.0 54 127.0 55 95.0 56 62.0 57 48.5 58 38.5 59 23.5 60 18.5 61 18.0 62 14.0 63 9.5 64 10.0 65 8.5 66 5.0 67 5.0 68 5.0 69 3.5 70 2.0 71 2.0 72 1.5 73 0.5 74 0.0 75 1.0 76 1.5 77 0.5 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0125 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0125 40-41 0.025 42-43 0.025 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.025 52-53 0.475 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 7.0 71 7.0 72 14.0 73 4.0 74 9.0 75 10.0 76 3.0 77 5.0 78 2.0 79 7.0 80 2.0 81 7.0 82 7.0 83 6.0 84 15.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 3895.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 79.225 #Duplication Level Percentage of deduplicated Percentage of total 1 92.74218996528873 73.475 2 3.9444619753865573 6.25 3 1.388450615336068 3.3000000000000003 4 0.5680025244556642 1.7999999999999998 5 0.347112653834017 1.375 6 0.06311139160618492 0.3 7 0.2208898706216472 1.225 8 0.09466708740927737 0.6 9 0.06311139160618492 0.44999999999999996 >10 0.5048911328494794 8.35 >50 0.06311139160618492 2.875 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 59 1.4749999999999999 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 56 1.4000000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 49 1.225 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 42 1.05 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 33 0.8250000000000001 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 31 0.775 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 24 0.6 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 22 0.5499999999999999 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 18 0.44999999999999996 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 17 0.42500000000000004 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 16 0.4 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 13 0.325 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 13 0.325 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 12 0.3 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 12 0.3 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 12 0.3 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 10 0.25 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 10 0.25 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 9 0.22499999999999998 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 9 0.22499999999999998 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 8 0.2 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 8 0.2 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 8 0.2 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 7 0.17500000000000002 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 7 0.17500000000000002 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 7 0.17500000000000002 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 7 0.17500000000000002 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 7 0.17500000000000002 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 7 0.17500000000000002 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 7 0.17500000000000002 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 6 0.15 No Hit GGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCA 6 0.15 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 5 0.125 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 5 0.125 No Hit GGAGGAGAGCGGCGGCGGTCTGTTCAAGATGGCTCAGGGCTTCATGAAGT 5 0.125 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 5 0.125 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 5 0.125 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 5 0.125 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 5 0.125 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 5 0.125 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 5 0.125 No Hit GGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTG 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.037500000000000006 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.075 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.075 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.0875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGATGA 15 9.0234715E-4 86.237495 1 GGGGAAG 15 9.0234715E-4 86.237495 1 AACTTCC 20 6.3262426E-4 45.388157 82-83 ACAACTT 20 6.3262426E-4 45.388157 80-81 ATGCTCA 20 6.752912E-4 44.798702 74-75 GCTCACA 20 6.752912E-4 44.798702 76-77 TAATGCT 20 7.202119E-4 44.22436 72-73 CGTAATG 20 7.202119E-4 44.22436 70-71 AACGTAA 20 7.67473E-4 43.664555 68-69 TGCACGA 20 8.1716344E-4 43.11875 62-63 CACGAAC 20 8.1716344E-4 43.11875 64-65 CGAACGT 20 8.1716344E-4 43.11875 66-67 GGAAGTA 20 8.1716344E-4 43.11875 54-55 CTTCCCT 25 0.0018966969 36.310524 84-85 TCCCTCT 25 0.0018966969 36.310524 86-87 TCACAAC 25 0.0019595933 36.073204 78-79 AAGTAAT 25 0.0024476151 34.495 56-57 GTCAAGG 25 0.0024476151 34.495 32-33 ATGGAAG 25 0.0024476151 34.495 52-53 AGGTCGC 25 0.0024476151 34.495 36-37 >>END_MODULE Rejected 198859 READS because READLEN < 1 Read 198859 spots for ERR6133511.sra Written 198859 spots for ERR6133511.sra Rejected 198859 READS because READLEN < 1 Read 198859 spots for ERR6133511.sra Written 198859 spots for ERR6133511.sra Rejected 198859 READS because READLEN < 1 Read 198859 spots for ERR6133511.sra Written 198859 spots for ERR6133511.sra Rejected 198859 READS because READLEN < 1 Read 198859 spots for ERR6133511.sra Written 198859 spots for ERR6133511.sra Rejected 198859 READS because READLEN < 1 Read 198859 spots for ERR6133511.sra Written 198859 spots for ERR6133511.sra Rejected 198859 READS because READLEN < 1 Read 198859 spots for ERR6133511.sra Written 198859 spots for ERR6133511.sra Rejected 198859 READS because READLEN < 1 Read 198859 spots for ERR6133511.sra Written 198859 spots for ERR6133511.sra Rejected 198859 READS because READLEN < 1 Read 198859 spots for ERR6133511.sra Written 198859 spots for ERR6133511.sra Rejected 198859 READS because READLEN < 1 Read 198859 spots for ERR6133511.sra Written 198859 spots for ERR6133511.sra Rejected 198859 READS because READLEN < 1 Read 198859 spots for ERR6133511.sra Written 198859 spots for ERR6133511.sra Rejected 198859 READS because READLEN < 1 Read 198859 spots for ERR6133511.sra Written 198859 spots for ERR6133511.sra Rejected 198859 READS because READLEN < 1 Read 198859 spots for ERR6133511.sra Written 198859 spots for ERR6133511.sra Rejected 198875 READS because READLEN < 1 Read 198875 spots for ERR6133511.sra Written 198875 spots for ERR6133511.sra Rejected 198859 READS because READLEN < 1 Read 198859 spots for ERR6133511.sra Written 198859 spots for ERR6133511.sra Rejected 198859 READS because READLEN < 1 Read 198859 spots for ERR6133511.sra Written 198859 spots for ERR6133511.sra Rejected 198859 READS because READLEN < 1 Read 198859 spots for ERR6133511.sra Written 198859 spots for ERR6133511.sra Rejected 198859 READS because READLEN < 1 Read 198859 spots for ERR6133511.sra Written 198859 spots for ERR6133511.sra Rejected 198859 READS because READLEN < 1 Read 198859 spots for ERR6133511.sra Written 198859 spots for ERR6133511.sra Rejected 198859 READS because READLEN < 1 Read 198859 spots for ERR6133511.sra Written 198859 spots for ERR6133511.sra Rejected 198859 READS because READLEN < 1 Read 198859 spots for ERR6133511.sra Written 198859 spots for ERR6133511.sra SRR ids: ['ERR6133511.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_vvyk5obn ERR6133511.sra spots: 3977196 blocks: [[1, 198859], [198860, 397718], [397719, 596577], [596578, 795436], [795437, 994295], [994296, 1193154], [1193155, 1392013], [1392014, 1590872], [1590873, 1789731], [1789732, 1988590], [1988591, 2187449], [2187450, 2386308], [2386309, 2585167], [2585168, 2784026], [2784027, 2982885], [2982886, 3181744], [3181745, 3380603], [3380604, 3579462], [3579463, 3778321], [3778322, 3977196]] ERR6133511 file size 879827 ERR6133511 completed basic pipeline successfully skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -q 10 -k inf -t 20 -o ERR6133511 ERR6133511_1.fastq Input file: ERR6133511_1.fastq trimmed: ERR6133511-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Sat Dec 7 07:38:04 2024 >> started Sat Dec 7 07:38:07 2024 >> done (2.944s) 3977196 reads processed; of these: 291 ( 0.01%) short reads filtered out after trimming by size control 16 ( 0.00%) empty reads filtered out after trimming by size control 3976889 (99.99%) reads available; of these: 17394 ( 0.44%) trimmed reads available after processing 3959495 (99.56%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 46 0.00% 19 45 0.00% 20 27 0.00% 21 23 0.00% 22 46 0.00% 23 15 0.00% 24 10 0.00% 25 19 0.00% 26 13 0.00% 27 22 0.00% 28 128 0.00% 29 53 0.00% 30 26 0.00% 31 24 0.00% 32 35 0.00% 33 35 0.00% 34 15 0.00% 35 149 0.00% 36 495 0.01% 37 23 0.00% 38 33 0.00% 39 55 0.00% 40 69 0.00% 41 50 0.00% 42 21 0.00% 43 12 0.00% 44 21 0.00% 45 7 0.00% 46 18 0.00% 47 9 0.00% 48 5 0.00% 49 9 0.00% 50 12 0.00% 51 54 0.00% 52 8 0.00% 53 11 0.00% 54 11 0.00% 55 16 0.00% 56 12 0.00% 57 20 0.00% 58 20 0.00% 59 11 0.00% 60 11 0.00% 61 12 0.00% 62 1 0.00% 63 0 0.00% 64 4 0.00% 65 2 0.00% 66 7 0.00% 67 8 0.00% 68 13 0.00% 69 65 0.00% 70 7934 0.20% 71 7417 0.19% 72 7609 0.19% 73 6965 0.18% 74 7099 0.18% 75 7192 0.18% 76 6541 0.16% 77 6508 0.16% 78 7214 0.18% 79 7918 0.20% 80 7497 0.19% 81 8601 0.22% 82 9765 0.25% 83 8950 0.23% 84 7978 0.20% 85 40 0.00% 86 78 0.00% 87 178 0.00% 88 293 0.01% 89 501 0.01% 90 1038 0.03% 91 2610 0.07% 92 10183 0.26% 93 3844924 96.68% 3976889 reads passed initial QC criterion=sequence-density sequence-density=0.44 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=32 prefix-density=0.44 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=24 fanout-score=247.27 fanout-score-rank=1 prefix-density=0.68 prefix-fanout=7.4 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAA Started job on | Dec 07 07:38:18 Started mapping on | Dec 07 07:38:18 Finished on | Dec 07 07:38:25 Mapping speed, Million of reads per hour | 2045.26 Number of input reads | 3976889 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2743957 Uniquely mapped reads % | 69.00% Average mapped length | 92.19 Number of splices: Total | 134060 Number of splices: Annotated (sjdb) | 111454 Number of splices: GT/AG | 128944 Number of splices: GC/AG | 3021 Number of splices: AT/AC | 78 Number of splices: Non-canonical | 2017 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.04% Deletion average length | 1.76 Insertion rate per base | 0.02% Insertion average length | 2.12 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1093691 % of reads mapped to multiple loci | 27.50% Number of reads mapped to too many loci | 26121 % of reads mapped to too many loci | 0.66% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.80% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 139241 139241 139241 N_multimapping 1093691 1093691 1093691 N_noFeature 186840 210741 2627095 N_ambiguous 105632 12639 333 UnstrandedReadsAssigned:2451485 PositiveStrandReadsAssigned:2520577 NegativeStrandReadsAssigned:116529 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133511 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 31 [index] number of targets: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in single-end mode [quant] will process file 1: ERR6133511-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,976,889 reads, 3,254,277 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,050 rounds 52973 ERR6133511.ke.tsv 35125 ERR6133511.se.tsv 88098 total ==> ERR6133511.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 121 35.5101 PNS24243 293 194 0 0 KQK14069 1603 1504 54 14.4566 KQK14071 474 375 0 0 ==> ERR6133511.se.tsv <== BRADI_1g14170v3 54 BRADI_1g53295v3 40 BRADI_1g59795v3 25 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 48 BRADI_1g74790v3 29 BRADI_1g09890v3 0 BRADI_1g77505v3 89 BRADI_1g48960v3 0 ERR6133511 completed mapping pipeline successfully